Package: patRoon
Type: Package
Title: Workflows for Mass-Spectrometry Based Non-Target Analysis
Version: 3.0.0
Authors@R: c(
    person("Rick", "Helmus",
           email = "r.helmus@uva.nl",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9401-3133")
    ),
    person("Olaf", "Brock",
           role = "ctb",
           comment = c(ORCID = "0000-0003-4727-8459")
    ),
    person("Vittorio", "Albergamo",
           role = "ctb",
           comment = c(ORCID = "0000-0002-5347-1362")
    ),
    person("Andrea", "Brunner",
           role = "ctb",
           comment = c(ORCID = "0000-0002-2801-1751")
    ),
    person("Emma", "Schymanski",
           role = "ctb",
           comment = c(ORCID = "0000-0001-6868-8145")
    ),
    person("Bas", "van de Velde",
           role = "ctb",
           comment = c(ORCID = "0000-0003-1292-3251"),
    ),
    person("Leon", "Saal",
           role = "ctb",
           comment = c(ORCID = "0000-0002-3522-7729"),
    ))
Description: Provides an easy-to-use interface to a mass spectrometry based
    non-target analysis workflow. Various (open-source) tools are combined
    which provide algorithms for extraction and grouping of features,
    extraction of MS and MS/MS data, automatic formula and compound annotation
    and grouping related features to components. In addition, various tools are
    provided for e.g. data preparation and cleanup, plotting results and
    automatic reporting.
License: GPL-3
LazyData: TRUE
RoxygenNote: 7.3.3
URL: https://github.com/rickhelmus/patRoon
BugReports: https://github.com/rickhelmus/patRoon/issues
Encoding: UTF-8
Depends: R (>= 4.1.0)
SystemRequirements: GNU make
Imports:
    methods,
    checkmate (>= 1.8.5),
    Rcpp,
    VennDiagram,
    UpSetR,
    stats,
    utils,
    parallel,
    grid,
    graphics,
    RColorBrewer,
    data.table (>= 1.15.0),
    withr,
    digest,
    DBI,
    RSQLite (>= 2.2.4),
    fst,
    processx,
    tools,
    MSnbase,
    Biobase,
    BiocParallel,
    xcms,
    cluster,
    fastcluster,
    gplots,
    heatmaply,
    dynamicTreeCut,
    dendextend,
    igraph,
    visNetwork,
    rJava,
    rcdk,
    fingerprint,
    mzR,
    circlize,
    miniUI,
    rhandsontable,
    rstudioapi,
    htmlwidgets,
    shiny,
    shinyjs,
    CAMERA,
    enviPat,
    knitr,
    rmarkdown,
    bslib (>= 0.9.0),
    bsicons,
    reactable (>= 0.4.1),
    magrittr,
    kableExtra,
    R.utils,
    magick,
    glue,
    jsonlite,
    Rdpack,
    rsm,
    future,
    future.apply,
    fs,
    yaml,
    keys,
    backports,
    httr,
    getPass,
    lzstring,
    constructive,
    signal,
    MBA
Suggests: 
    RDCOMClient,
    metfRag,
    enviPick,
    nontarget,
    RAMClustR,
    cliqueMS,
    KPIC,
    MetaClean,
    MetaCleanData,
    testthat,
    rlang,
    vdiffr,
    patRoonData,
    devtools,
    covr,
    DiagrammeR,
    DiagrammeRsvg,
    rsvg,
    pkgload,
    splashR,
    MS2Quant,
    MS2Tox,
    ChemmineR,
    fmcsR,
    reticulate,
    Rmstoolkitlib
LinkingTo:
    Rcpp,
    rapidjsonr
Config/testthat/edition: 3
Config/testthat/parallel: true
Config/testthat/start-first: feature*, screening, compounds, components, tp, formulas, pred, mspeaklists, project-tool, report
RdMacros:
    Rdpack
Collate: 
    'RcppExports.R'
    'generics.R'
    'cache.R'
    'main.R'
    'workflow-step.R'
    'TP.R'
    'TP-structure.R'
    'TP-CTS.R'
    'TP-ann_comp.R'
    'TP-formula.R'
    'TP-ann_form.R'
    'TP-biotransformer.R'
    'TP-library.R'
    'TP-library_formula.R'
    'features.R'
    'workflow-step-set.R'
    'features-set.R'
    'feature_groups.R'
    'feature_groups-set.R'
    'TP-logic.R'
    'utils.R'
    'utils-adduct.R'
    'adduct.R'
    'analysisInfo.R'
    'check_ui.R'
    'utils-components.R'
    'components.R'
    'check_components.R'
    'check_features.R'
    'components-camera.R'
    'components-features.R'
    'components-cliquems.R'
    'components-clust.R'
    'components-intclust.R'
    'components-set.R'
    'components-nontarget.R'
    'components-nontarget-set.R'
    'components-openms.R'
    'components-ramclustr.R'
    'components-specclust.R'
    'feature_annotations.R'
    'formulas.R'
    'mspeaklists.R'
    'compounds.R'
    'utils-compounds.R'
    'utils-screening.R'
    'feature_groups-screening.R'
    'feature_groups-screening-set.R'
    'components-tps.R'
    'compounds-cluster.R'
    'mslibrary.R'
    'compounds-library.R'
    'compounds-metfrag.R'
    'utils-feat_annotations-set.R'
    'compounds-set.R'
    'utils-sirius.R'
    'compounds-sirius.R'
    'convert.R'
    'defunct.R'
    'utils-bruker.R'
    'deprecated-formulas-bruker.R'
    'deprecated-mspeaklists-bruker.R'
    'deprecated-mspeaklists-mzr.R'
    'deprecated.R'
    'utils-IPO.R'
    'doe-optimizer.R'
    'eic_eim_gui.R'
    'feature_groups-ADT.R'
    'feature_groups-bruker.R'
    'feature_groups-comparison.R'
    'feature_groups-envimass.R'
    'feature_groups-filter.R'
    'feature_groups-greedy.R'
    'feature_groups-ims.R'
    'feature_groups-kpic2.R'
    'feature_groups-openms.R'
    'feature_groups-optimize.R'
    'feature_groups-optimize-kpic2.R'
    'feature_groups-optimize-openms.R'
    'feature_groups-optimize-xcms.R'
    'feature_groups-optimize-xcms3.R'
    'feature_groups-plot.R'
    'feature_groups-sirius.R'
    'feature_groups-table.R'
    'feature_groups-tasq.R'
    'feature_groups-xcms.R'
    'feature_groups-xcms3.R'
    'features-bruker.R'
    'features-envipick.R'
    'features-kpic2.R'
    'features-openms.R'
    'features-optimize.R'
    'features-optimize-envipick.R'
    'features-optimize-kpic2.R'
    'features-optimize-openms.R'
    'features-optimize-xcms.R'
    'features-optimize-xcms3.R'
    'features-piek.R'
    'features-safd.R'
    'features-sirius.R'
    'features-table.R'
    'features-tasq.R'
    'features-xcms.R'
    'features-xcms3.R'
    'formulas-genform.R'
    'formulas-set.R'
    'formulas-sirius.R'
    'limits.R'
    'msdata.R'
    'mslibrary-json.R'
    'mslibrary-msp.R'
    'mspeaklists-set.R'
    'multi-process-classic.R'
    'multi-process-future.R'
    'multi-process.R'
    'peaks.R'
    'project-tool-analyses.R'
    'project-tool-annotation.R'
    'project-tool-features.R'
    'project-tool-gen.R'
    'project-tool-general.R'
    'project-tool-pre_treatment.R'
    'project-tool-report.R'
    'project-tool-tp.R'
    'project-tool-utils.R'
    'project-tool.R'
    'report-html.R'
    'report-html-TPs.R'
    'report-html-components.R'
    'report-html-feat_annotations.R'
    'report-html-features.R'
    'report-html-utils.R'
    'report-legacy.R'
    'report.R'
    'utils-TPs.R'
    'utils-checkmate.R'
    'utils-exported.R'
    'utils-feat_annotations.R'
    'utils-features-ims.R'
    'utils-features-sets.R'
    'utils-features.R'
    'utils-formulas.R'
    'utils-mol.R'
    'utils-msdata.R'
    'utils-mslibrary.R'
    'utils-mspeaklists.R'
    'utils-optimize.R'
    'utils-plot.R'
    'utils-progress.R'
    'utils-sets.R'
    'utils-xcms.R'
    'zzz.R'
VignetteBuilder: knitr
